Changes between Version 13 and Version 14 of SOPs/mapping

Timestamp:

01/15/14 14:11:19 (11 years ago)

Author:

gbell

Comment:

--

SOPs/mapping

@@ -49 +49 @@
 
 bowtie2 can also perform local alignments where the unaligned end(s) of a read are clipped (so, for example, remaining adapter won't prevent alignment) by adding the argument '''--local'''.
+
+'''[http://bio-bwa.sourceforge.net/ bwa - Burrows-Wheeler Alignment Tool ]'''
+
+Bwa is a software package containing several related algorithms using the Burrows-Wheeler Transform.  It works well even with indels, but not with spliced (RNA) reads. 
+
+Sample commands for sort (<70 nt) reads:
+{{{
+# Align single reads
+bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.sai"
+bsub "bwa samse /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.sai Reads.fq > Reads.bwa.sam"
+# Align paired-end reads
+bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.1.fq > Mapped_reads.1.sai"
+bsub "bwa aln /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.2.fq > Mapped_reads.2.sai"
+bsub "bwa sampe /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Mapped_reads.1.sai Mapped_reads.2.sai Reads.1.fq Reads.2.fq > Reads.bwa.sam"
+}}}
+
+Sample commands for long (70 nt - 1M nt) reads:
+{{{
+# Align single reads
+bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.fq > Mapped_reads.bwa.sam"
+# Align paired-end reads
+bsub "bwa mem /nfs/genomes/mouse_gp_jul_07_no_random/bwa/mm9 Reads.1.fq Reads.1.fq > Mapped_reads.bwa.sam"
+}}}
 
 '''Other tools'''